Merge branch 'development' of magit1.mpie.de:damask/DAMASK into development
This commit is contained in:
Martin Diehl
commit
89107eaff9
|
|
@ -21,13 +21,13 @@ if not os.path.isdir(binDir):
|
|||
|
||||
#define ToDo list
|
||||
processing_subDirs = ['pre','post','misc',]
|
||||
processing_extensions = ['.py',]
|
||||
processing_extensions = ['.py','.sh',]
|
||||
|
||||
for subDir in processing_subDirs:
|
||||
theDir = os.path.abspath(os.path.join(baseDir,subDir))
|
||||
|
||||
for theFile in os.listdir(theDir):
|
||||
if os.path.splitext(theFile)[1] in processing_extensions: # omit anything not fitting our script extensions (skip .py.bak, .py~, and the like)
|
||||
if os.path.splitext(theFile)[1] in processing_extensions: # only consider files with proper extensions
|
||||
|
||||
src = os.path.abspath(os.path.join(theDir,theFile))
|
||||
sym_link = os.path.abspath(os.path.join(binDir,os.path.splitext(theFile)[0]))
|
||||
|
|
|
|||
|
|
@ -166,14 +166,6 @@ for name in filenames:
|
|||
np.zeros((table.data.shape[0],
|
||||
3-table.data[:,9:].shape[1]),dtype='f'))) # fill coords up to 3D with zeros
|
||||
|
||||
if remarks != []: damask.util.croak(remarks)
|
||||
if errors != []:
|
||||
damask.util.croak(errors)
|
||||
table.close(dismiss = True)
|
||||
continue
|
||||
|
||||
# --------------- figure out size and grid ---------------------------------------------------------
|
||||
|
||||
coords = [np.unique(table.data[:,9+i]) for i in xrange(3)]
|
||||
mincorner = np.array(map(min,coords))
|
||||
maxcorner = np.array(map(max,coords))
|
||||
|
|
|
|||
|
|
@ -88,16 +88,27 @@ Add column(s) containing Euclidean distance to grain structural features: bounda
|
|||
|
||||
""", version = scriptID)
|
||||
|
||||
parser.add_option('-c','--coordinates', dest='coords', metavar='string',
|
||||
help='column label of coordinates [%default]')
|
||||
parser.add_option('-i','--identifier', dest='id', metavar = 'string',
|
||||
help='column label of grain identifier [%default]')
|
||||
parser.add_option('-t','--type', dest = 'type', action = 'extend', metavar = '<string LIST>',
|
||||
help = 'feature type {%s} '%(', '.join(map(lambda x:'/'.join(x['names']),features))) )
|
||||
parser.add_option('-n','--neighborhood',dest='neighborhood', choices = neighborhoods.keys(), metavar = 'string',
|
||||
help = 'type of neighborhood [neumann] {%s}'%(', '.join(neighborhoods.keys())))
|
||||
parser.add_option('-s', '--scale', dest = 'scale', type = 'float', metavar = 'float',
|
||||
parser.add_option('-p',
|
||||
'--pos', '--position',
|
||||
dest = 'coords', metavar = 'string',
|
||||
help = 'label of coordinates [%default]')
|
||||
parser.add_option('-i',
|
||||
'--id', '--identifier',
|
||||
dest = 'id', metavar = 'string',
|
||||
help='label of grain identifier [%default]')
|
||||
parser.add_option('-t',
|
||||
'--type',
|
||||
dest = 'type', action = 'extend', metavar = '<string LIST>',
|
||||
help = 'feature type {{{}}} '.format(', '.join(map(lambda x:'/'.join(x['names']),features))) )
|
||||
parser.add_option('-n',
|
||||
'--neighborhood',
|
||||
dest = 'neighborhood', choices = neighborhoods.keys(), metavar = 'string',
|
||||
help = 'neighborhood type [neumann] {{{}}}'.format(', '.join(neighborhoods.keys())))
|
||||
parser.add_option('-s',
|
||||
'--scale',
|
||||
dest = 'scale', type = 'float', metavar = 'float',
|
||||
help = 'voxel size [%default]')
|
||||
|
||||
parser.set_defaults(coords = 'pos',
|
||||
id = 'texture',
|
||||
neighborhood = 'neumann',
|
||||
|
|
@ -111,7 +122,7 @@ if options.type is None:
|
|||
if not set(options.type).issubset(set(list(itertools.chain(*map(lambda x: x['names'],features))))):
|
||||
parser.error('type must be chosen from (%s).'%(', '.join(map(lambda x:'|'.join(x['names']),features))) )
|
||||
if 'biplane' in options.type and 'boundary' in options.type:
|
||||
parser.error("only one from aliases 'biplane' and 'boundary' possible.")
|
||||
parser.error('only one from aliases "biplane" and "boundary" possible.')
|
||||
|
||||
feature_list = []
|
||||
for i,feature in enumerate(features):
|
||||
|
|
@ -172,9 +183,7 @@ for name in filenames:
|
|||
|
||||
N = grid.prod()
|
||||
|
||||
if N != len(table.data): errors.append('data count {} does not match grid '.format(N) +
|
||||
'x'.join(map(str,grid)) +
|
||||
'.')
|
||||
if N != len(table.data): errors.append('data count {} does not match grid {}.'.format(N,'x'.join(map(str,grid))))
|
||||
if errors != []:
|
||||
damask.util.croak(errors)
|
||||
table.close(dismiss = True)
|
||||
|
|
|
|||
|
|
@ -0,0 +1,56 @@
|
|||
#!/usr/bin/env python
|
||||
# -*- coding: UTF-8 no BOM -*-
|
||||
|
||||
import os
|
||||
from optparse import OptionParser
|
||||
import damask
|
||||
|
||||
scriptName = os.path.splitext(os.path.basename(__file__))[0]
|
||||
scriptID = ' '.join([scriptName,damask.version])
|
||||
|
||||
|
||||
# --------------------------------------------------------------------
|
||||
# MAIN
|
||||
# --------------------------------------------------------------------
|
||||
|
||||
parser = OptionParser(option_class=damask.extendableOption, usage='%prog options file[s]', description = """
|
||||
Add info lines to ASCIItable header.
|
||||
|
||||
""", version = scriptID)
|
||||
|
||||
parser.add_option('-i',
|
||||
'--info',
|
||||
dest = 'info', action = 'extend', metavar = '<string LIST>',
|
||||
help = 'items to add')
|
||||
|
||||
parser.set_defaults(info = [],
|
||||
)
|
||||
|
||||
(options,filenames) = parser.parse_args()
|
||||
|
||||
# --- loop over input files ------------------------------------------------------------------------
|
||||
|
||||
if filenames == []: filenames = [None]
|
||||
|
||||
for name in filenames:
|
||||
try: table = damask.ASCIItable(name = name,
|
||||
buffered = False)
|
||||
except: continue
|
||||
damask.util.report(scriptName,name)
|
||||
|
||||
# ------------------------------------------ assemble header ---------------------------------------
|
||||
|
||||
table.head_read()
|
||||
table.info_append(options.info)
|
||||
table.head_write()
|
||||
|
||||
# ------------------------------------------ pass through data -------------------------------------
|
||||
|
||||
outputAlive = True
|
||||
|
||||
while outputAlive and table.data_read(): # read next data line of ASCII table
|
||||
outputAlive = table.data_write() # output processed line
|
||||
|
||||
# ------------------------------------------ output finalization -----------------------------------
|
||||
|
||||
table.close() # close ASCII tables
|
||||
|
|
@ -127,7 +127,7 @@ for name in filenames:
|
|||
# ------------------------------------------ output result ---------------------------------------
|
||||
|
||||
if name:
|
||||
writer = vtk.vtkXMLPolyDataWriter()
|
||||
writer = vtk.vtkXMLRectilinearGridWriter()
|
||||
writer.SetCompressorTypeToZLib()
|
||||
writer.SetDataModeToBinary()
|
||||
writer.SetFileName(os.path.join(os.path.split(name)[0],
|
||||
|
|
|
|||
|
|
@ -1,108 +0,0 @@
|
|||
#!/usr/bin/env python
|
||||
# -*- coding: UTF-8 no BOM -*-
|
||||
|
||||
import os,sys,vtk
|
||||
import numpy as np
|
||||
from optparse import OptionParser
|
||||
import damask
|
||||
|
||||
scriptName = os.path.splitext(os.path.basename(__file__))[0]
|
||||
scriptID = ' '.join([scriptName,damask.version])
|
||||
|
||||
#--------------------------------------------------------------------------------------------------
|
||||
# MAIN
|
||||
#--------------------------------------------------------------------------------------------------
|
||||
|
||||
parser = OptionParser(option_class=damask.extendableOption, usage='%prog [file[s]]', description = """
|
||||
Produce VTK rectilinear mesh of structure data from geom description
|
||||
|
||||
""", version = scriptID)
|
||||
|
||||
parser.add_option('-m','--nodata',
|
||||
dest = 'data',
|
||||
action = 'store_false',
|
||||
help = 'generate mesh without microstructure index data')
|
||||
|
||||
parser.set_defaults(data = True,
|
||||
)
|
||||
|
||||
(options, filenames) = parser.parse_args()
|
||||
|
||||
# --- loop over input files -------------------------------------------------------------------------
|
||||
|
||||
if filenames == []: filenames = [None]
|
||||
|
||||
for name in filenames:
|
||||
try:
|
||||
table = damask.ASCIItable(name = name,
|
||||
buffered = False, labeled = False, readonly = True)
|
||||
except: continue
|
||||
damask.util.report(scriptName,name)
|
||||
|
||||
# --- interpret header ----------------------------------------------------------------------------
|
||||
|
||||
table.head_read()
|
||||
info,extra_header = table.head_getGeom()
|
||||
|
||||
damask.util.croak(['grid a b c: %s'%(' x '.join(map(str,info['grid']))),
|
||||
'size x y z: %s'%(' x '.join(map(str,info['size']))),
|
||||
'origin x y z: %s'%(' : '.join(map(str,info['origin']))),
|
||||
'homogenization: %i'%info['homogenization'],
|
||||
'microstructures: %i'%info['microstructures'],
|
||||
])
|
||||
|
||||
errors = []
|
||||
if np.any(info['grid'] < 1): errors.append('invalid grid a b c.')
|
||||
if np.any(info['size'] <= 0.0): errors.append('invalid size x y z.')
|
||||
|
||||
#--- read microstructure information --------------------------------------------------------------
|
||||
|
||||
if options.data:
|
||||
microstructure,ok = table.microstructure_read(info['grid'],strict = True) # read microstructure
|
||||
|
||||
if ok:
|
||||
structure = vtk.vtkIntArray()
|
||||
structure.SetName('Microstructures')
|
||||
for idx in microstructure: structure.InsertNextValue(idx)
|
||||
|
||||
else: errors.append('mismatch between data and grid dimension.')
|
||||
|
||||
if errors != []:
|
||||
damask.util.croak(errors)
|
||||
table.close(dismiss = True)
|
||||
continue
|
||||
|
||||
# --- generate VTK rectilinear grid ---------------------------------------------------------------
|
||||
|
||||
grid = vtk.vtkRectilinearGrid()
|
||||
grid.SetDimensions([x+1 for x in info['grid']])
|
||||
for i in xrange(3):
|
||||
temp = vtk.vtkDoubleArray()
|
||||
temp.SetNumberOfTuples(info['grid'][i]+1)
|
||||
for j in xrange(info['grid'][i]+1):
|
||||
temp.InsertTuple1(j,j*info['size'][i]/info['grid'][i]+info['origin'][i])
|
||||
if i == 0: grid.SetXCoordinates(temp)
|
||||
elif i == 1: grid.SetYCoordinates(temp)
|
||||
elif i == 2: grid.SetZCoordinates(temp)
|
||||
|
||||
|
||||
if options.data: grid.GetCellData().AddArray(structure)
|
||||
|
||||
# --- write data -----------------------------------------------------------------------------------
|
||||
if name:
|
||||
writer = vtk.vtkXMLRectilinearGridWriter()
|
||||
(directory,filename) = os.path.split(name)
|
||||
writer.SetDataModeToBinary()
|
||||
writer.SetCompressorTypeToZLib()
|
||||
writer.SetFileName(os.path.join(directory,os.path.splitext(filename)[0]+'.'+writer.GetDefaultFileExtension()))
|
||||
else:
|
||||
writer = vtk.vtkDataSetWriter()
|
||||
writer.WriteToOutputStringOn()
|
||||
writer.SetHeader('# powered by '+scriptID)
|
||||
|
||||
if vtk.VTK_MAJOR_VERSION <= 5: writer.SetInput(grid)
|
||||
else: writer.SetInputData(grid)
|
||||
writer.Write()
|
||||
if name is None: sys.stdout.write(writer.GetOutputString()[0:writer.GetOutputStringLength()])
|
||||
|
||||
table.close()
|
||||
|
|
@ -0,0 +1,15 @@
|
|||
#!/bin/bash
|
||||
|
||||
for geom in "$@"
|
||||
do
|
||||
vtk_rectilinearGrid \
|
||||
--geom $geom
|
||||
|
||||
geom_toTable \
|
||||
< $geom \
|
||||
| \
|
||||
vtk_addRectilinearGridData \
|
||||
--scalar microstructure \
|
||||
--inplace \
|
||||
--vtk ${geom%.*}.vtr
|
||||
done
|
||||
|
|
@ -1,125 +0,0 @@
|
|||
#!/usr/bin/env python
|
||||
# -*- coding: UTF-8 no BOM -*-
|
||||
|
||||
import os,sys,vtk
|
||||
import numpy as np
|
||||
import damask
|
||||
from optparse import OptionParser
|
||||
|
||||
scriptName = os.path.splitext(os.path.basename(__file__))[0]
|
||||
scriptID = ' '.join([scriptName,damask.version])
|
||||
|
||||
#--------------------------------------------------------------------------------------------------
|
||||
# MAIN
|
||||
#--------------------------------------------------------------------------------------------------
|
||||
parser = OptionParser(option_class=damask.extendableOption, usage='%prog [seedsfile[s]]', description = """
|
||||
Produce VTK point mesh from seeds file
|
||||
|
||||
""", version = scriptID)
|
||||
|
||||
parser.add_option('-s', '--size',
|
||||
dest = 'size',
|
||||
type = 'float', nargs = 3, metavar = 'float float float',
|
||||
help = 'x,y,z size of hexahedral box [1.0 along largest grid point number]')
|
||||
parser.add_option('-p','--position',
|
||||
dest = 'position',
|
||||
type = 'string', metavar = 'string',
|
||||
help = 'column label for coordinates [%default]')
|
||||
|
||||
parser.set_defaults(size = [0.0,0.0,0.0],
|
||||
position = 'pos',
|
||||
)
|
||||
|
||||
(options, filenames) = parser.parse_args()
|
||||
|
||||
# --- loop over input files -------------------------------------------------------------------------
|
||||
|
||||
if filenames == []: filenames = [None]
|
||||
|
||||
for name in filenames:
|
||||
try:
|
||||
table = damask.ASCIItable(name = name,
|
||||
buffered = False, readonly = True)
|
||||
except: continue
|
||||
damask.util.report(scriptName,name)
|
||||
|
||||
# --- interpret header ----------------------------------------------------------------------------
|
||||
|
||||
table.head_read()
|
||||
info,extra_header = table.head_getGeom()
|
||||
|
||||
damask.util.croak(['grid a b c: %s'%(' x '.join(map(str,info['grid']))),
|
||||
'size x y z: %s'%(' x '.join(map(str,info['size']))),
|
||||
'origin x y z: %s'%(' : '.join(map(str,info['origin']))),
|
||||
'homogenization: %i'%info['homogenization'],
|
||||
'microstructures: %i'%info['microstructures'],
|
||||
])
|
||||
|
||||
remarks = []
|
||||
errors = []
|
||||
|
||||
if np.any(info['grid'] < 1): remarks.append('invalid grid a b c.')
|
||||
if np.any(info['size'] <= 0.0) \
|
||||
and np.all(info['grid'] < 1): errors.append('invalid size x y z.')
|
||||
else:
|
||||
for i in xrange(3):
|
||||
if info['size'][i] <= 0.0: # any invalid size?
|
||||
info['size'][i] = float(info['grid'][i])/max(info['grid']) # normalize to grid
|
||||
remarks.append('rescaling size {} to {}...'.format({0:'x',1:'y',2:'z'}[i],info['size'][i]))
|
||||
if table.label_dimension(options.position) != 3:
|
||||
errors.append('columns "{}" have dimension {}'.format(options.position,table.label_dimension(options.position)))
|
||||
if remarks != []: damask.util.croak(remarks)
|
||||
if errors != []:
|
||||
damask.util.croak(errors)
|
||||
table.close(dismiss=True)
|
||||
continue
|
||||
|
||||
labels = ['{dim}_{label}'.format(dim = 1+i,label = options.position) for i in xrange(3)]
|
||||
hasGrains = table.label_index('microstructure') != -1
|
||||
labels += ['microstructure'] if hasGrains else []
|
||||
|
||||
table.data_readArray(labels) # read ASCIItable columns
|
||||
|
||||
coords = table.data[:,:3]*info['size'] # assign coordinates (rescaled to box size)
|
||||
grain = table.data[:,3].astype('i') if hasGrains else 1+np.arange(len(coords),dtype='i') # assign grains
|
||||
|
||||
# --- generate grid --------------------------------------------------------------------------------
|
||||
|
||||
grid = vtk.vtkUnstructuredGrid()
|
||||
pts = vtk.vtkPoints()
|
||||
|
||||
# --- process microstructure information -----------------------------------------------------------
|
||||
|
||||
IDs = vtk.vtkIntArray()
|
||||
IDs.SetNumberOfComponents(1)
|
||||
IDs.SetName("GrainID")
|
||||
|
||||
for i,item in enumerate(coords):
|
||||
IDs.InsertNextValue(grain[i])
|
||||
pid = pts.InsertNextPoint(item[0:3])
|
||||
pointIds = vtk.vtkIdList()
|
||||
pointIds.InsertId(0, pid)
|
||||
grid.InsertNextCell(1, pointIds)
|
||||
|
||||
grid.SetPoints(pts)
|
||||
grid.GetCellData().AddArray(IDs)
|
||||
|
||||
#--- write data -----------------------------------------------------------------------------------
|
||||
if name:
|
||||
writer = vtk.vtkXMLRectilinearGridWriter()
|
||||
(directory,filename) = os.path.split(name)
|
||||
writer.SetDataModeToBinary()
|
||||
writer.SetCompressorTypeToZLib()
|
||||
writer.SetFileName(os.path.join(directory,os.path.splitext(filename)[0]+'.'+writer.GetDefaultFileExtension()))
|
||||
else:
|
||||
writer = vtk.vtkDataSetWriter()
|
||||
writer.WriteToOutputStringOn()
|
||||
writer.SetHeader('# powered by '+scriptID)
|
||||
|
||||
if vtk.VTK_MAJOR_VERSION <= 5: writer.SetInput(grid)
|
||||
else: writer.SetInputData(grid)
|
||||
writer.Write()
|
||||
if name is None: sys.stdout.write(writer.GetOutputString()[0:writer.GetOutputStringLength()])
|
||||
|
||||
table.close()
|
||||
|
||||
|
|
@ -0,0 +1,12 @@
|
|||
#!/bin/bash
|
||||
|
||||
for seeds in "$@"
|
||||
do
|
||||
vtk_pointcloud $seeds
|
||||
|
||||
vtk_addPointCloudData $seeds \
|
||||
--scalar microstructure,weight \
|
||||
--inplace \
|
||||
--vtk ${seeds%.*}.vtp \
|
||||
|
||||
done
|
||||
|
|
@ -14,26 +14,30 @@ scriptID = ' '.join([scriptName,damask.version])
|
|||
#--------------------------------------------------------------------------------------------------
|
||||
|
||||
parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [file[s]]', description = """
|
||||
Create seed file taking microstructure indices from given geom file but excluding black-listed grains.
|
||||
Create seed file taking microstructure indices from given geom file.
|
||||
Indices can be black-listed or white-listed.
|
||||
|
||||
""", version = scriptID)
|
||||
|
||||
parser.add_option('-w','--white',
|
||||
action = 'extend', metavar='<int LIST>',
|
||||
parser.add_option('-w',
|
||||
'--white',
|
||||
action = 'extend', metavar = '<int LIST>',
|
||||
dest = 'whitelist',
|
||||
help = 'whitelist of grain IDs')
|
||||
parser.add_option('-b','--black',
|
||||
action = 'extend', metavar='<int LIST>',
|
||||
parser.add_option('-b',
|
||||
'--black',
|
||||
action = 'extend', metavar = '<int LIST>',
|
||||
dest = 'blacklist',
|
||||
help = 'blacklist of grain IDs')
|
||||
parser.add_option('-p','--position',
|
||||
parser.add_option('-p',
|
||||
'--pos', '--seedposition',
|
||||
dest = 'position',
|
||||
type = 'string', metavar = 'string',
|
||||
help = 'column label for coordinates [%default]')
|
||||
help = 'label of coordinates [%default]')
|
||||
|
||||
parser.set_defaults(whitelist = [],
|
||||
blacklist = [],
|
||||
position = 'pos',
|
||||
pos = 'pos',
|
||||
)
|
||||
|
||||
(options,filenames) = parser.parse_args()
|
||||
|
|
@ -46,25 +50,18 @@ options.blacklist = map(int,options.blacklist)
|
|||
if filenames == []: filenames = [None]
|
||||
|
||||
for name in filenames:
|
||||
try:
|
||||
table = damask.ASCIItable(name = name,
|
||||
outname = os.path.splitext(name)[0]+'.seeds' if name else name,
|
||||
buffered = False, labeled = False)
|
||||
except:
|
||||
continue
|
||||
try: table = damask.ASCIItable(name = name,
|
||||
outname = os.path.splitext(name)[0]+'.seeds' if name else name,
|
||||
buffered = False,
|
||||
labeled = False)
|
||||
except: continue
|
||||
damask.util.report(scriptName,name)
|
||||
|
||||
# --- interpret header ----------------------------------------------------------------------------
|
||||
|
||||
table.head_read()
|
||||
info,extra_header = table.head_getGeom()
|
||||
|
||||
damask.util.croak(['grid a b c: %s'%(' x '.join(map(str,info['grid']))),
|
||||
'size x y z: %s'%(' x '.join(map(str,info['size']))),
|
||||
'origin x y z: %s'%(' : '.join(map(str,info['origin']))),
|
||||
'homogenization: %i'%info['homogenization'],
|
||||
'microstructures: %i'%info['microstructures'],
|
||||
])
|
||||
damask.util.report_geom(info)
|
||||
|
||||
errors = []
|
||||
if np.any(info['grid'] < 1): errors.append('invalid grid a b c.')
|
||||
|
|
@ -98,14 +95,14 @@ for name in filenames:
|
|||
table.info_clear()
|
||||
table.info_append(extra_header+[
|
||||
scriptID + ' ' + ' '.join(sys.argv[1:]),
|
||||
"grid\ta {grid[0]}\tb {grid[1]}\tc {grid[2]}".format(grid=info['grid']),
|
||||
"size\tx {size[0]}\ty {size[1]}\tz {size[2]}".format(size=info['size']),
|
||||
"origin\tx {origin[0]}\ty {origin[1]}\tz {origin[2]}".format(origin=info['origin']),
|
||||
"homogenization\t{homog}".format(homog=info['homogenization']),
|
||||
"microstructures\t{microstructures}".format(microstructures=info['microstructures']),
|
||||
"grid\ta {}\tb {}\tc {}".format(*info['grid']),
|
||||
"size\tx {}\ty {}\tz {}".format(*info['size']),
|
||||
"origin\tx {}\ty {}\tz {}".format(*info['origin']),
|
||||
"homogenization\t{}".format(info['homogenization']),
|
||||
"microstructures\t{}".format(info['microstructures']),
|
||||
])
|
||||
table.labels_clear()
|
||||
table.labels_append(['{dim}_{label}'.format(dim = 1+i,label = options.position) for i in range(3)]+['microstructure'])
|
||||
table.labels_append(['{dim}_{label}'.format(dim = 1+i,label = options.pos) for i in range(3)]+['microstructure'])
|
||||
table.head_write()
|
||||
table.output_flush()
|
||||
|
||||
|
|
|
|||
Loading…
Reference in New Issue